Files and code used for de Mendoza et al 2019 "Convergent evolution of a vertebrate-like methylome in a marine sponge". Nature Ecology and Evolution 2019 Oct;3(10):1464-1473. doi: 10.1038/s41559-019-0983-2
Free access to the manuscript: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31558833/.
Code
- Master_Script_deMendozaNEE.R
Files
SequenceAlignments.zip: Amino acid sequence alignments of DNMT1, DNMT3, TET and UHRF1.Aqu2.1.genes.bed.gz: Amphimedon queenslandica Aqu2.1 gene annotation.Amphimedon_queenslandica.NNNNstrech.bed.gz: Regions encompassing Ns (gaps) in the Amphimedon genome assembly.bacterial_contigs: list of Amphimedon assembly contigs from bacterial origin.Amphimedon_UMR_LMR.zip: Output files from MethylSeekR UMR/LMR finding for each developmental sample.Amphimedon_DAPseq_TF_motifs.zip: Best motif as identified by HOMER2 for Amphimedon Transcription Factors DAP-seq/ampDAP-seq experiments.Amphimedon_DSS_DMRs.zip: Output files from DSS DMR calling across all developmental stages.CELSEQ_Aqu2.summarised.tsv.gz: Mean CEL-seq TPM summarised values for the developmental stages, from GSE70185.hmC_150windows_both_stages_01.bed.gz: Regions with hmCG/CG >= 0.1 in both Precompetent larva and juvenile stages.